Package: EnrichmentBrowser 2.37.0

Ludwig Geistlinger

EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

Authors:Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Mirko Signorelli [ctb], Rohit Satyam [ctb], Marcel Ramos [ctb], Levi Waldron [ctb], Ralf Zimmer [aut]

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EnrichmentBrowser.pdf |EnrichmentBrowser.html✨
EnrichmentBrowser/json (API)
NEWS

# Install 'EnrichmentBrowser' in R:
install.packages('EnrichmentBrowser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lgeistlinger/enrichmentbrowser/issues

On BioConductor:EnrichmentBrowser-2.37.0(bioc 3.21)EnrichmentBrowser-2.36.0(bioc 3.20)

immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwriting

9.35 score 20 stars 3 packages 155 scripts 949 downloads 12 mentions 29 exports 87 dependencies

Last updated 23 days agofrom:0601e6c423. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:combResultscompileGRNconfigEBrowserdeAnadownloadPathwayseaBrowseebrowserexprsHeatmapgetGenesetsggeaGraphggeaGraphLegendgsRankingidMapidTypesimportisAvailablemakeExampleDatanbeanbeaMethodsnormalizepdistrprobe2genereadSEsbeasbeaMethodsshowAvailableCollectionsshowAvailableSpeciesvolcanowriteGMT

Dependencies:abindannotateAnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyredgeRfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueGO.dbgraphgraphiteGSEABasehttrhwriterIRangesjsonliteKEGGgraphKEGGRESTlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpillarpkgconfigplogrpngpurrrR6rappdirsRCurlRgraphvizrlangRSQLiteS4ArraysS4VectorssafeSparseArraySparseMSPIAstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxtableXVectorzlibbioc

Seamless navigation through combined results of set- & network-based enrichment analysis

Ludwig Geistlinger

Rendered fromEnrichmentBrowser.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-07-30
Started: 2023-07-17

Readme and manuals

Help Manual

Help pageTopics
Combining enrichment analysis resultscomb.ea.results combResults
Compilation of a gene regulatory network from pathway databasescompile.grn.from.kegg compileGRN
Configuring the EnrichmentBrowserconfig.ebrowser configEBrowser
Differential expression analysis between two sample groupsde.ana deAna
Download of KEGG pathways for a particular organismdownload.kegg.pathways downloadPathways
Exploration of enrichment analysis resultsea.browse eaBrowse gs.ranking gsRanking
Seamless navigation through enrichment analysis resultsebrowser
Export results from set- and network-based enrichment analysisexport
Definition of gene sets according to different sourcesget.go.genesets get.kegg.genesets getGenesets parse.genesets.from.GMT showAvailableCollections showAvailableSpecies writeGMT
GGEA graphs of consistency between regulation and expressionggea.graph ggea.graph.legend ggeaGraph ggeaGraphLegend
Mapping between gene ID typesidMap idTypes map.ids
Import results from differential expression (DE) analysisimport
Is a required package available?isAvailable
Example data for the EnrichmentBrowser packagemakeExampleData
Network-based enrichment analysis (NBEA)ggea nbea nbeaMethods spia
Normalization of microarray and RNA-seq expression datanormalize
Visualization of gene expressionexprsHeatmap pdistr plots volcano
Transformation of probe level expression to gene level expressionprobe.2.gene.eset probe2gene
Reading gene expression data from fileread.eset readSE
Set-based enrichment analysis (SBEA)gsea ora sbea sbeaMethods